Paquet : libgenomicsdb-java (1.5.4-1)

Liens pour libgenomicsdb-java

Ressources Debian :

Télécharger le paquet source genomicsdb :

Responsables :

Ressources externes :

Page d'accueil [www.genomicsdb.org]

Paquets similaires :

sparse array storage library for genomics (Java library)

GenomicsDB is built on top of a htslib fork and an internal array storage system for importing, querying and transforming variant data. Variant data is sparse by nature (sparse relative to the whole genome) and using sparse array data stores is a perfect fit for storing such data.

The GenomicsDB stores variant data in a 2D array where:

 - Each column corresponds to a genomic position (chromosome + position);
 - Each row corresponds to a sample in a VCF (or CallSet in the GA4GH
   terminology);
 - Each cell contains data for a given sample/CallSet at a given position;
   data is stored in the form of cell attributes;
 - Cells are stored in column major order - this makes accessing cells with
   the same column index (i.e. data for a given genomic position over all
   samples) fast.
 - Variant interval/gVCF interval data is stored in a cell at the start of the
   interval. The END is stored as a cell attribute. For variant intervals
   (such as deletions and gVCF REF blocks), an additional cell is stored at
   the END value of the variant interval. When queried for a given genomic
   position, the query library performs an efficient sweep to determine all
   intervals that intersect with the queried position.

This package contains the Java library.

Autres paquets associés à libgenomicsdb-java

dépendances

recommandations

suggestions

enhances

dep: libcommons-io-java (>= 2.17.0)

Common useful IO related classes
dep: libgenomicsdb-jni (<< 1.5.4-1.1~)

sparse array storage library for genomics (Java native bindings)

dep: libgenomicsdb-jni (>= 1.5.4-1)
dep: libgetopt-java

GNU getopt - Java port
dep: libgoogle-gson-java

Converts Java objects into their JSON representation
dep: libguava-java

Suite of Google common libraries for Java
dep: libhtsjdk-java (>= 3.0.2)

Java API for high-throughput sequencing data (HTS) formats
dep: libjson-simple-java

Simple, lightweight and efficient JSON toolkit for Java
dep: liblog4j2-java (>= 2.19.0)

Apache Log4j - Logging Framework for Java
dep: libprotobuf-java

Java bindings for protocol buffers

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